X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FUserDefinedColours.java;h=1836e33b3d35d70ee0f1b783ba785f840bb4603d;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=8deec8e4f51bc8b4c6d1c0baf4d2ba9f1444883a;hpb=174230b4233d9ce80f94527768d2cd2f76da11ab;p=jalview.git diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java index 8deec8e..1836e33 100755 --- a/src/jalview/gui/UserDefinedColours.java +++ b/src/jalview/gui/UserDefinedColours.java @@ -1,682 +1,921 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA - */ -package jalview.gui; - -import jalview.datamodel.*; - -import jalview.io.*; - -import jalview.jbgui.*; - -import jalview.schemes.*; - -import java.awt.*; -import java.awt.event.*; - -import java.io.*; - -import java.util.*; - -import javax.swing.*; -import javax.swing.event.*; - - - -/** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ -public class UserDefinedColours extends GUserDefinedColours - implements ChangeListener -{ - AlignmentPanel ap; - SequenceGroup seqGroup; - Vector selectedButtons; - ColourSchemeI oldColourScheme; - JInternalFrame frame; - MCview.PDBCanvas pdbcanvas; - - /** - * Creates a new UserDefinedColours object. - * - * @param ap DOCUMENT ME! - * @param sg DOCUMENT ME! - */ - public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg) - { - super(); - frame = new JInternalFrame(); - frame.setContentPane(this); - Desktop.addInternalFrame(frame, "User Defined Colours", 720, 370, true); - - if (System.getProperty("os.name").startsWith("Mac")) - { - frame.setSize(760, 370); - } - - if (sg != null) - { - frame.setTitle(frame.getTitle() + " (" + sg.getName() + ")"); - } - - colorChooser.getSelectionModel().addChangeListener(this); - - this.ap = ap; - seqGroup = sg; - - if (seqGroup != null) - { - oldColourScheme = seqGroup.cs; - } - else - { - oldColourScheme = ap.av.getGlobalColourScheme(); - } - - if (oldColourScheme instanceof UserColourScheme) - { - schemeName.setText( ( (UserColourScheme) oldColourScheme).getName()); - } - for (int i = 0; i < 20; i++) - { - makeButton(ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i]) + - "", ResidueProperties.aa[i]); - } - - makeButton("B", "B"); - makeButton("Z", "Z"); - makeButton("X", "X"); - makeButton("Gap", "-"); - } - - public UserDefinedColours(MCview.PDBCanvas pdb, ColourSchemeI oldcs) - { - super(); - frame = new JInternalFrame(); - frame.setContentPane(this); - Desktop.addInternalFrame(frame, "User Defined Colours", 720, 370, true); - pdbcanvas = pdb; - - if (System.getProperty("os.name").startsWith("Mac")) - { - frame.setSize(760, 370); - } - - colorChooser.getSelectionModel().addChangeListener(this); - - oldColourScheme = oldcs; - - if (oldColourScheme instanceof UserColourScheme) - { - schemeName.setText( ( (UserColourScheme) oldColourScheme).getName()); - } - for (int i = 0; i < 20; i++) - { - makeButton(ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i]) + - "", ResidueProperties.aa[i]); - } - - makeButton("B", "B"); - makeButton("Z", "Z"); - makeButton("X", "X"); - makeButton("Gap", "-"); - } - - - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void stateChanged(ChangeEvent evt) - { - if (selectedButtons != null) - { - JButton button; - for(int i=0; i0) - start = (JButton)selectedButtons.elementAt(selectedButtons.size()-1); - else - start = (JButton) e.getSource(); - - int startIndex=0, endIndex=0; - for(int b=0; b endIndex) - { - int temp = startIndex; - startIndex = endIndex; - endIndex = temp; - } - - for(int b=startIndex; b<=endIndex; b++) - { - JButton button = (JButton)buttonPanel.getComponent(b); - if(!selectedButtons.contains(button)) - { - button.setForeground(button.getBackground().brighter().brighter()); - selectedButtons.add(button); - } - } - } - else if(!e.isControlDown()) - { - for(int b=0; b0) - colorChooser.setColor( ((JButton)selectedButtons.elementAt(0)).getBackground()); - } - - /** - * DOCUMENT ME! - * - * @param label DOCUMENT ME! - * @param aa DOCUMENT ME! - */ - void makeButton(String label, String aa) - { - final JButton button = new JButton(); - Color col = Color.white; - - try - { - col = oldColourScheme.findColour(aa, -1); - } - catch (Exception ex) - { - // ex.printStackTrace(); - } - - button.setBackground(col); - button.setText(label); - button.setForeground(col.darker().darker().darker()); - button.setFont(new java.awt.Font("Verdana", 1, 10)); - button.addMouseListener(new java.awt.event.MouseAdapter() - { - public void mouseClicked(MouseEvent e) - { - colourButtonPressed(e); - } - }); - - buttonPanel.add(button, null); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void okButton_actionPerformed(ActionEvent e) - { - applyButton_actionPerformed(null); - - try - { - frame.setClosed(true); - } - catch (Exception ex) - { - } - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void applyButton_actionPerformed(ActionEvent e) - { - UserColourScheme ucs = getSchemeFromGUI(); - ucs.setName(schemeName.getText()); - - if (seqGroup != null) - { - seqGroup.cs = ucs; - ap.repaint(); - } - else if(ap!=null) - { - ap.alignFrame.changeColour(ucs); - } - else if(pdbcanvas!=null) - { - pdbcanvas.pdb.setColours(ucs); - pdbcanvas.updateSeqColours(); - } - } - - UserColourScheme getSchemeFromGUI() - { - Color[] newColours = new Color[24]; - - for (int i = 0; i < 24; i++) - { - JButton button = (JButton) buttonPanel.getComponent(i); - newColours[i] = button.getBackground(); - } - - UserColourScheme ucs = new UserColourScheme(newColours); - if(ap!=null) - ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus()); - - - return ucs; - } - - - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void loadbutton_actionPerformed(ActionEvent e) - { - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty( - "LAST_DIRECTORY"), new String[] { "jc" }, - new String[] { "Jalview User Colours" }, "Jalview User Colours"); - chooser.setFileView(new jalview.io.JalviewFileView()); - chooser.setDialogTitle("Load colour scheme"); - chooser.setToolTipText("Load"); - - int value = chooser.showOpenDialog(this); - - if (value == JalviewFileChooser.APPROVE_OPTION) - { - File choice = chooser.getSelectedFile(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent()); - String defaultColours = jalview.bin.Cache.getDefault("USER_DEFINED_COLOURS", - choice.getPath()); - if (defaultColours.indexOf(choice.getPath()) == -1) - defaultColours = defaultColours.concat("|").concat(choice.getPath()); - - jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours); - - - UserColourScheme ucs = loadColours(choice.getAbsolutePath()); - Color[] colors = ucs.getColours(); - schemeName.setText(ucs.getName()); - - for (int i = 0; i < colors.length; i++) - { - JButton button = (JButton) buttonPanel.getComponent(i); - button.setBackground(colors[i]); - } - } - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public static UserColourScheme loadDefaultColours() - { - UserColourScheme ret = null; - - String colours = jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS"); - if ( colours != null ) - { - if(colours.indexOf("|")>-1) - colours = colours.substring(0, colours.indexOf("|")); - - ret = loadColours(colours); - } - - if(ret == null) - { - Color[] newColours = new Color[24]; - for (int i = 0; i < 24; i++) - { - newColours[i] = Color.white; - } - ret = new UserColourScheme(newColours); - } - - return ret; - } - - /** - * DOCUMENT ME! - * - * @param file DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - static UserColourScheme loadColours(String file) - { - UserColourScheme ucs = null; - Color[] newColours = null; - - try - { - InputStreamReader in = new InputStreamReader(new FileInputStream( - file), "UTF-8"); - - jalview.schemabinding.version2.JalviewUserColours jucs - = new jalview.schemabinding.version2.JalviewUserColours(); - - org.exolab.castor.xml.Unmarshaller unmar - = new org.exolab.castor.xml.Unmarshaller(jucs); - jucs = (jalview.schemabinding.version2.JalviewUserColours) unmar.unmarshal( in ); - - newColours = new Color[jucs.getColourCount()]; - - for (int i = 0; i < 24; i++) - { - newColours[i] = new Color(Integer.parseInt( - jucs.getColour(i).getRGB(), 16)); - } - if (newColours != null) - { - ucs = new UserColourScheme(newColours); - ucs.setName( jucs.getSchemeName() ); - } - - } - catch (Exception ex) - { - //Could be Archive Jalview format - try{ - InputStreamReader in = new InputStreamReader(new FileInputStream( - file), "UTF-8"); - - jalview.binding.JalviewUserColours jucs - = new jalview.binding.JalviewUserColours(); - - jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in); - - newColours = new Color[jucs.getColourCount()]; - - for (int i = 0; i < 24; i++) - { - newColours[i] = new Color(Integer.parseInt( - jucs.getColour(i).getRGB(), 16)); - } - if (newColours != null) - { - ucs = new UserColourScheme(newColours); - ucs.setName(jucs.getSchemeName()); - } - }catch(Exception ex2) - { ex2.printStackTrace(); } - - if(newColours==null) - System.out.println("Error loading User ColourFile\n"+ex); - } - - return ucs; - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void savebutton_actionPerformed(ActionEvent e) - { - if(schemeName.getText().trim().length()<1) - { - JOptionPane.showInternalMessageDialog(Desktop.desktop, - "User colour scheme must have a name!", - "No name for colour scheme", - JOptionPane.WARNING_MESSAGE); - return; - } - - if(userColourSchemes!=null && userColourSchemes.containsKey(schemeName.getText()) ) - { - int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop, "Colour scheme "+schemeName.getText()+ " exists." - +"\nContinue saving colour scheme as "+schemeName.getText()+"?", - "Duplicate scheme name", JOptionPane.YES_NO_OPTION); - if(reply != JOptionPane.YES_OPTION) - return; - - userColourSchemes.remove(schemeName.getText()); - } - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty( - "LAST_DIRECTORY"), new String[] { "jc" }, - new String[] { "Jalview User Colours" }, "Jalview User Colours"); - - chooser.setFileView(new jalview.io.JalviewFileView()); - chooser.setDialogTitle("Save colour scheme"); - chooser.setToolTipText("Save"); - - int value = chooser.showSaveDialog(this); - - if (value == JalviewFileChooser.APPROVE_OPTION) - { - String choice = chooser.getSelectedFile().getPath(); - String defaultColours = jalview.bin.Cache.getDefault("USER_DEFINED_COLOURS", choice); - if(defaultColours.indexOf(choice)==-1) - { - if(defaultColours.length()>0) - defaultColours = defaultColours.concat("|"); - defaultColours = defaultColours.concat(choice); - } - - userColourSchemes.put(schemeName.getText(), getSchemeFromGUI()); - - ap.alignFrame.updateUserColourMenu(); - - jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours); - - jalview.binding.JalviewUserColours ucs = new jalview.binding.JalviewUserColours(); - ucs.setSchemeName(schemeName.getText()); - try - { - PrintWriter out = new PrintWriter(new OutputStreamWriter( - new FileOutputStream(choice), "UTF-8")); - - for (int i = 0; i < 24; i++) - { - JButton button = (JButton) buttonPanel.getComponent(i); - jalview.binding.Colour col = new jalview.binding.Colour(); - col.setName(button.getText()); - col.setRGB(jalview.util.Format.getHexString( - button.getBackground())); - ucs.addColour(col); - } - - ucs.marshal(out); - out.close(); - } - catch (Exception ex) - { - ex.printStackTrace(); - } - } - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void cancelButton_actionPerformed(ActionEvent e) - { - if (ap != null) - { - if (seqGroup != null) - { - seqGroup.cs = oldColourScheme; - } - else if (ap != null) - { - ap.av.setGlobalColourScheme(oldColourScheme); - } - ap.repaint(); - } - - if(pdbcanvas!=null) - { - pdbcanvas.pdb.setColours(oldColourScheme); - } - - try - { - frame.setClosed(true); - } - catch (Exception ex) - { - } - } - - - static Hashtable userColourSchemes; - - public static Hashtable getUserColourSchemes() - { - return userColourSchemes; - } - - public static void initUserColourSchemes(String files) - { - userColourSchemes = new Hashtable(); - - if(files==null || files.length()==0) - return; - - - // In case colours can't be loaded, we'll remove them - // from the default list here. - StringBuffer coloursFound = new StringBuffer(); - StringTokenizer st = new StringTokenizer(files, "|"); - while (st.hasMoreElements()) - { - String file = st.nextToken(); - try - { - UserColourScheme ucs = loadColours(file); - if (ucs != null) - { - if (coloursFound.length() > 0) - coloursFound.append("|"); - coloursFound.append(file); - userColourSchemes.put(ucs.getName(), ucs); - } - } - catch (Exception ex) - { - System.out.println("Error loading User ColourFile\n" + ex); - } - } - if (!files.equals(coloursFound.toString())) - { - if (coloursFound.toString().length() > 1) - jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", - coloursFound.toString()); - else - jalview.bin.Cache.applicationProperties.remove("USER_DEFINED_COLOURS"); - } - } - - public static void removeColourFromDefaults(String target) - { - // The only way to find colours by name is to load them in - // In case colours can't be loaded, we'll remove them - // from the default list here. - - userColourSchemes = new Hashtable(); - - StringBuffer coloursFound = new StringBuffer(); - StringTokenizer st = new StringTokenizer( - jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS"), "|"); - - while (st.hasMoreElements()) - { - String file = st.nextToken(); - try - { - UserColourScheme ucs = loadColours(file); - if (ucs != null && !ucs.getName().equals(target)) - { - if (coloursFound.length() > 0) - coloursFound.append("|"); - coloursFound.append(file); - userColourSchemes.put(ucs.getName(), ucs); - } - } - catch (Exception ex) - { - System.out.println("Error loading User ColourFile\n" + ex); - } - } - - if (coloursFound.toString().length() > 1) - jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", coloursFound.toString()); - else - jalview.bin.Cache.applicationProperties.remove("USER_DEFINED_COLOURS"); - - } -} +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.gui; + +import java.util.Locale; + +import jalview.bin.Cache; +import jalview.io.JalviewFileChooser; +import jalview.io.JalviewFileView; +import jalview.jbgui.GUserDefinedColours; +import jalview.schemes.ColourSchemeI; +import jalview.schemes.ColourSchemeLoader; +import jalview.schemes.ColourSchemes; +import jalview.schemes.ResidueProperties; +import jalview.schemes.UserColourScheme; +import jalview.util.ColorUtils; +import jalview.util.Format; +import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.xml.binding.jalview.JalviewUserColours; +import jalview.xml.binding.jalview.JalviewUserColours.Colour; +import jalview.xml.binding.jalview.ObjectFactory; + +import java.awt.Color; +import java.awt.Font; +import java.awt.Insets; +import java.awt.event.MouseAdapter; +import java.awt.event.MouseEvent; +import java.io.File; +import java.io.FileOutputStream; +import java.io.OutputStreamWriter; +import java.io.PrintWriter; +import java.util.ArrayList; +import java.util.List; + +import javax.swing.JButton; +import javax.swing.JInternalFrame; +import javax.swing.event.ChangeEvent; +import javax.swing.event.ChangeListener; +import javax.xml.bind.JAXBContext; +import javax.xml.bind.Marshaller; + +/** + * This panel allows the user to assign colours to Amino Acid residue codes, and + * save the colour scheme. + * + * @author Andrew Waterhouse + * @author Mungo Carstairs + */ +public class UserDefinedColours extends GUserDefinedColours + implements ChangeListener +{ + private static final Font VERDANA_BOLD_10 = new Font("Verdana", Font.BOLD, + 10); + + public static final String USER_DEFINED_COLOURS = "USER_DEFINED_COLOURS"; + + private static final String LAST_DIRECTORY = "LAST_DIRECTORY"; + + private static final int MY_FRAME_HEIGHT = 440; + + private static final int MY_FRAME_WIDTH = 810; + + private static final int MY_FRAME_WIDTH_CASE_SENSITIVE = 970; + + AlignmentPanel ap; + + /* + * the colour scheme when the dialog was opened, or + * the scheme last saved to file + */ + ColourSchemeI oldColourScheme; + + /* + * flag is true if the colour scheme has been changed since the + * dialog was opened, or the changes last saved to file + */ + boolean changedButNotSaved; + + JInternalFrame frame; + + List upperCaseButtons; + + List lowerCaseButtons; + + /** + * Creates and displays a new UserDefinedColours panel + * + * @param alignPanel + */ + public UserDefinedColours(AlignmentPanel alignPanel) + { + this(); + + lcaseColour.setEnabled(false); + + this.ap = alignPanel; + + oldColourScheme = alignPanel.av.getGlobalColourScheme(); + + if (oldColourScheme instanceof UserColourScheme) + { + schemeName.setText(oldColourScheme.getSchemeName()); + if (((UserColourScheme) oldColourScheme) + .getLowerCaseColours() != null) + { + caseSensitive.setSelected(true); + lcaseColour.setEnabled(true); + resetButtonPanel(true); + } + else + { + resetButtonPanel(false); + } + } + else + { + resetButtonPanel(false); + } + + showFrame(); + } + + UserDefinedColours() + { + super(); + selectedButtons = new ArrayList<>(); + } + + void showFrame() + { + colorChooser.getSelectionModel().addChangeListener(this); + frame = new JInternalFrame(); + frame.setContentPane(this); + Desktop.addInternalFrame(frame, + MessageManager.getString("label.user_defined_colours"), + MY_FRAME_WIDTH, MY_FRAME_HEIGHT, true); + } + + /** + * Rebuilds the panel with coloured buttons for residues. If not case + * sensitive colours, show 3-letter amino acid code as button text. If case + * sensitive, just show the single letter code, in order to make space for the + * additional buttons. + * + * @param isCaseSensitive + */ + void resetButtonPanel(boolean isCaseSensitive) + { + buttonPanel.removeAll(); + + if (upperCaseButtons == null) + { + upperCaseButtons = new ArrayList<>(); + } + + for (int i = 0; i < 20; i++) + { + String label = isCaseSensitive ? ResidueProperties.aa[i] + : ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i]) + .toString(); + JButton button = makeButton(label, ResidueProperties.aa[i], + upperCaseButtons, i); + buttonPanel.add(button); + } + + buttonPanel.add(makeButton("B", "B", upperCaseButtons, 20)); + buttonPanel.add(makeButton("Z", "Z", upperCaseButtons, 21)); + buttonPanel.add(makeButton("X", "X", upperCaseButtons, 22)); + buttonPanel.add(makeButton("Gap", "-", upperCaseButtons, 23)); + + if (!isCaseSensitive) + { + gridLayout.setRows(6); + gridLayout.setColumns(4); + } + else + { + gridLayout.setRows(7); + int cols = 7; + gridLayout.setColumns(cols + 1); + + if (lowerCaseButtons == null) + { + lowerCaseButtons = new ArrayList<>(); + } + + for (int i = 0; i < 20; i++) + { + int row = i / cols + 1; + int index = (row * cols) + i; + JButton button = makeButton( + ResidueProperties.aa[i].toLowerCase(Locale.ROOT), + ResidueProperties.aa[i].toLowerCase(Locale.ROOT), + lowerCaseButtons, i); + + buttonPanel.add(button, index); + } + } + + if (isCaseSensitive) + { + buttonPanel.add(makeButton("b", "b", lowerCaseButtons, 20)); + buttonPanel.add(makeButton("z", "z", lowerCaseButtons, 21)); + buttonPanel.add(makeButton("x", "x", lowerCaseButtons, 22)); + } + + // JAL-1360 widen the frame dynamically to accommodate case-sensitive AA + // codes + if (this.frame != null) + { + int newWidth = isCaseSensitive ? MY_FRAME_WIDTH_CASE_SENSITIVE + : MY_FRAME_WIDTH; + this.frame.setSize(newWidth, this.frame.getHeight()); + } + + buttonPanel.validate(); + validate(); + } + + /** + * ChangeListener handler for when a colour is picked in the colour chooser. + * The action is to apply the colour to all selected buttons as their + * background colour. Foreground colour (text) is set to a lighter shade in + * order to highlight which buttons are selected. If 'Lower Case Colour' is + * active, then the colour is applied to all lower case buttons (as well as + * the Lower Case Colour button itself). + * + * @param evt + */ + @Override + public void stateChanged(ChangeEvent evt) + { + JButton button = null; + final Color newColour = colorChooser.getColor(); + if (lcaseColour.isSelected()) + { + selectedButtons.clear(); + for (int i = 0; i < lowerCaseButtons.size(); i++) + { + button = lowerCaseButtons.get(i); + button.setBackground(newColour); + button.setForeground( + ColorUtils.brighterThan(button.getBackground())); + } + } + for (int i = 0; i < selectedButtons.size(); i++) + { + button = selectedButtons.get(i); + button.setBackground(newColour); + button.setForeground(ColorUtils.brighterThan(newColour)); + } + + changedButNotSaved = true; + } + + /** + * Performs actions when a residue button is clicked. This manages the button + * selection set (highlighted by brighter foreground text). + *

+ * On select button(s) with Ctrl/click or Shift/click: set button foreground + * text to brighter than background. + *

+ * On unselect button(s) with Ctrl/click on selected, or click to release + * current selection: reset foreground text to darker than background. + *

+ * Simple click: clear selection (resetting foreground to darker); set clicked + * button foreground to brighter + *

+ * Finally, synchronize the colour chooser to the colour of the first button + * in the selected set. + * + * @param e + */ + public void colourButtonPressed(MouseEvent e) + { + JButton pressed = (JButton) e.getSource(); + + if (e.isShiftDown()) + { + JButton start, end = (JButton) e.getSource(); + if (selectedButtons.size() > 0) + { + start = selectedButtons.get(selectedButtons.size() - 1); + } + else + { + start = (JButton) e.getSource(); + } + + int startIndex = 0, endIndex = 0; + for (int b = 0; b < buttonPanel.getComponentCount(); b++) + { + if (buttonPanel.getComponent(b) == start) + { + startIndex = b; + } + if (buttonPanel.getComponent(b) == end) + { + endIndex = b; + } + } + + if (startIndex > endIndex) + { + int temp = startIndex; + startIndex = endIndex; + endIndex = temp; + } + + for (int b = startIndex; b <= endIndex; b++) + { + JButton button = (JButton) buttonPanel.getComponent(b); + if (!selectedButtons.contains(button)) + { + button.setForeground( + ColorUtils.brighterThan(button.getBackground())); + selectedButtons.add(button); + } + } + } + else if (!e.isControlDown()) + { + for (int b = 0; b < selectedButtons.size(); b++) + { + JButton button = selectedButtons.get(b); + button.setForeground(ColorUtils.darkerThan(button.getBackground())); + } + selectedButtons.clear(); + pressed.setForeground( + ColorUtils.brighterThan(pressed.getBackground())); + selectedButtons.add(pressed); + + } + else if (e.isControlDown()) + { + if (selectedButtons.contains(pressed)) + { + pressed.setForeground( + ColorUtils.darkerThan(pressed.getBackground())); + selectedButtons.remove(pressed); + } + else + { + pressed.setForeground( + ColorUtils.brighterThan(pressed.getBackground())); + selectedButtons.add(pressed); + } + } + + if (selectedButtons.size() > 0) + { + colorChooser.setColor((selectedButtons.get(0)).getBackground()); + } + } + + /** + * A helper method to update or make a colour button, whose background colour + * is the associated colour, and text colour a darker shade of the same. If + * the button is already in the list, then its text and margins are updated, + * if not then it is created and added. This method supports toggling between + * case-sensitive and case-insensitive button panels. The case-sensitive + * version has abbreviated button text in order to fit in more buttons. + * + * @param label + * @param residue + * @param the + * list of buttons + * @param buttonIndex + * the button's position in the list + */ + JButton makeButton(String label, String residue, List buttons, + int buttonIndex) + { + final JButton button; + Color col; + + if (buttonIndex < buttons.size()) + { + button = buttons.get(buttonIndex); + col = button.getBackground(); + } + else + { + button = new JButton(); + button.addMouseListener(new MouseAdapter() + { + @Override + public void mouseClicked(MouseEvent e) + { + colourButtonPressed(e); + } + }); + + buttons.add(button); + + /* + * make initial button colour that of the current colour scheme, + * if it is a simple per-residue colouring, else white + */ + col = Color.white; + if (oldColourScheme != null && oldColourScheme.isSimple()) + { + col = oldColourScheme.findColour(residue.charAt(0), 0, null, null, + 0f); + } + } + + if (caseSensitive.isSelected()) + { + button.setMargin(new Insets(2, 2, 2, 2)); + } + else + { + button.setMargin(new Insets(2, 14, 2, 14)); + } + + button.setOpaque(true); // required for the next line to have effect + button.setBackground(col); + button.setText(label); + button.setForeground(ColorUtils.darkerThan(col)); + button.setFont(VERDANA_BOLD_10); + + return button; + } + + /** + * On 'OK', check that at least one colour has been assigned to a residue (and + * if not issue a warning), and apply the chosen colour scheme and close the + * panel. + */ + @Override + protected void okButton_actionPerformed() + { + if (isNoSelectionMade()) + { + JvOptionPane.showMessageDialog(Desktop.desktop, + MessageManager + .getString("label.no_colour_selection_in_scheme"), + MessageManager.getString("label.no_colour_selection_warn"), + JvOptionPane.WARNING_MESSAGE); + } + else + { + /* + * OK is treated as 'apply colours and close' + */ + applyButton_actionPerformed(); + + /* + * If editing a named colour scheme, warn if changes + * have not been saved + */ + warnIfUnsavedChanges(); + + try + { + frame.setClosed(true); + } catch (Exception ex) + { + } + } + } + + /** + * If we have made changes to an existing user defined colour scheme but not + * saved them, show a dialog with the option to save. If the user chooses to + * save, do so, else clear the colour scheme name to indicate a new colour + * scheme. + */ + protected void warnIfUnsavedChanges() + { + // BH 2018 no warning in JavaScript TODO + + if (!Platform.isJS() && changedButNotSaved) + /** + * Java only + * + * @j2sIgnore + */ + { + String name = schemeName.getText().trim(); + if (oldColourScheme != null && !"".equals(name) + && name.equals(oldColourScheme.getSchemeName())) + { + String message = MessageManager + .formatMessage("label.scheme_changed", name); + String title = MessageManager.getString("label.save_changes"); + String[] options = new String[] { title, + MessageManager.getString("label.dont_save_changes"), }; + final String question = JvSwingUtils.wrapTooltip(true, message); + int response = JvOptionPane.showOptionDialog(Desktop.desktop, + question, title, JvOptionPane.DEFAULT_OPTION, + JvOptionPane.PLAIN_MESSAGE, null, options, options[0]); + + if (response == 0) + { + /* + * prompt to save changes to file; if done, + * resets 'changed' flag to false + */ + savebutton_actionPerformed(); + } + + /* + * if user chooses not to save (either in this dialog or in the + * save as dialogs), treat this as a new user defined colour scheme + */ + if (changedButNotSaved) + { + /* + * clear scheme name and re-apply as an anonymous scheme + */ + schemeName.setText(""); + applyButton_actionPerformed(); + } + } + } + } + + /** + * Returns true if the user has not made any colour selection (including if + * 'case-sensitive' selected and no lower-case colour chosen). + * + * @return + */ + protected boolean isNoSelectionMade() + { + final boolean noUpperCaseSelected = upperCaseButtons == null + || upperCaseButtons.isEmpty(); + final boolean noLowerCaseSelected = caseSensitive.isSelected() + && (lowerCaseButtons == null || lowerCaseButtons.isEmpty()); + final boolean noSelectionMade = noUpperCaseSelected + || noLowerCaseSelected; + return noSelectionMade; + } + + /** + * Applies the current colour scheme to the alignment or sequence group + */ + @Override + protected void applyButton_actionPerformed() + { + if (isNoSelectionMade()) + { + JvOptionPane.showMessageDialog(Desktop.desktop, + MessageManager + .getString("label.no_colour_selection_in_scheme"), + MessageManager.getString("label.no_colour_selection_warn"), + JvOptionPane.WARNING_MESSAGE); + + } + UserColourScheme ucs = getSchemeFromButtons(); + + ap.alignFrame.changeColour(ucs); + } + + /** + * Constructs an instance of UserColourScheme with the residue colours + * currently set on the buttons on the panel + * + * @return + */ + UserColourScheme getSchemeFromButtons() + { + + Color[] newColours = new Color[24]; + + int length = upperCaseButtons.size(); + if (length < 24) + { + int i = 0; + for (JButton btn : upperCaseButtons) + { + newColours[i] = btn.getBackground(); + i++; + } + } + else + { + for (int i = 0; i < 24; i++) + { + JButton button = upperCaseButtons.get(i); + newColours[i] = button.getBackground(); + } + } + + UserColourScheme ucs = new UserColourScheme(newColours); + ucs.setName(schemeName.getText()); + + if (caseSensitive.isSelected()) + { + newColours = new Color[23]; + length = lowerCaseButtons.size(); + if (length < 23) + { + int i = 0; + for (JButton btn : lowerCaseButtons) + { + newColours[i] = btn.getBackground(); + i++; + } + } + else + { + for (int i = 0; i < 23; i++) + { + JButton button = lowerCaseButtons.get(i); + newColours[i] = button.getBackground(); + } + } + ucs.setLowerCaseColours(newColours); + } + + return ucs; + } + + /** + * Action on clicking Load scheme button. + *

    + *
  • Open a file chooser to browse for files with extension .jc
    • + *
  • Load in the colour scheme and transfer it to this panel's buttons
    • + *
  • Register the loaded colour scheme
    • + *
+ */ + @Override + protected void loadbutton_actionPerformed() + { + upperCaseButtons = new ArrayList<>(); + lowerCaseButtons = new ArrayList<>(); + JalviewFileChooser chooser = new JalviewFileChooser("jc", + "Jalview User Colours"); + chooser.setFileView(new JalviewFileView()); + chooser.setDialogTitle( + MessageManager.getString("label.load_colour_scheme")); + chooser.setToolTipText(MessageManager.getString("action.load")); + chooser.setResponseHandler(0, new Runnable() + { + @Override + public void run() + { + File choice = chooser.getSelectedFile(); + Cache.setProperty(LAST_DIRECTORY, choice.getParent()); + + UserColourScheme ucs = ColourSchemeLoader + .loadColourScheme(choice.getAbsolutePath()); + Color[] colors = ucs.getColours(); + schemeName.setText(ucs.getSchemeName()); + + if (ucs.getLowerCaseColours() != null) + { + caseSensitive.setSelected(true); + lcaseColour.setEnabled(true); + resetButtonPanel(true); + for (int i = 0; i < lowerCaseButtons.size(); i++) + { + JButton button = lowerCaseButtons.get(i); + button.setBackground(ucs.getLowerCaseColours()[i]); + } + } + else + { + caseSensitive.setSelected(false); + lcaseColour.setEnabled(false); + resetButtonPanel(false); + } + + for (int i = 0; i < upperCaseButtons.size(); i++) + { + JButton button = upperCaseButtons.get(i); + button.setBackground(colors[i]); + } + + addNewColourScheme(choice.getPath()); + } + }); + + chooser.showOpenDialog(this); + } + + /** + * Loads the user-defined colour scheme from the first file listed in property + * "USER_DEFINED_COLOURS". If this fails, returns an all-white colour scheme. + * + * @return + */ + public static UserColourScheme loadDefaultColours() + { + UserColourScheme ret = null; + + String colours = Cache.getProperty(USER_DEFINED_COLOURS); + if (colours != null) + { + if (colours.indexOf("|") > -1) + { + colours = colours.substring(0, colours.indexOf("|")); + } + ret = ColourSchemeLoader.loadColourScheme(colours); + } + + if (ret == null) + { + ret = new UserColourScheme("white"); + } + + return ret; + } + + /** + * Action on pressing the Save button. + *
    + *
  • Check a name has been entered
    • + *
  • Warn if the name already exists, remove any existing scheme of the same + * name if overwriting
    • + *
  • Do the standard file chooser thing to write with extension .jc
    • + *
  • If saving changes (possibly not yet applied) to the currently selected + * colour scheme, then apply the changes, as it is too late to back out + * now
    • + *
  • Don't apply the changes if the currently selected scheme is different, + * to allow a new scheme to be configured and saved but not applied
    • + *
+ * If the scheme is saved to file, the 'changed' flag field is reset to false. + */ + @Override + protected void savebutton_actionPerformed() + { + String name = schemeName.getText().trim(); + if (name.length() < 1) + { + JvOptionPane.showInternalMessageDialog(Desktop.desktop, + MessageManager + .getString("label.user_colour_scheme_must_have_name"), + MessageManager.getString("label.no_name_colour_scheme"), + JvOptionPane.WARNING_MESSAGE); + } + + if (!Platform.isJS() && ColourSchemes.getInstance().nameExists(name)) + { + /** + * java only + * + * @j2sIgnore + */ + { + int reply = JvOptionPane.showInternalConfirmDialog(Desktop.desktop, + MessageManager.formatMessage( + "label.colour_scheme_exists_overwrite", new Object[] + { name, name }), + MessageManager.getString("label.duplicate_scheme_name"), + JvOptionPane.YES_NO_OPTION); + if (reply != JvOptionPane.YES_OPTION) + { + return; + } + } + } + + JalviewFileChooser chooser = new JalviewFileChooser("jc", + "Jalview User Colours"); + + JalviewFileView fileView = new JalviewFileView(); + chooser.setFileView(fileView); + chooser.setDialogTitle( + MessageManager.getString("label.save_colour_scheme")); + chooser.setToolTipText(MessageManager.getString("action.save")); + int option = chooser.showSaveDialog(this); + if (option == JalviewFileChooser.APPROVE_OPTION) + { + File file = chooser.getSelectedFile(); + UserColourScheme updatedScheme = addNewColourScheme(file.getPath()); + saveToFile(file); + changedButNotSaved = false; + + /* + * changes saved - apply to alignment if we are changing + * the currently selected colour scheme; also make the updated + * colours the 'backout' scheme on Cancel + */ + if (oldColourScheme != null + && name.equals(oldColourScheme.getSchemeName())) + { + oldColourScheme = updatedScheme; + applyButton_actionPerformed(); + } + } + } + + /** + * Adds the current colour scheme to the Jalview properties file so it is + * loaded on next startup, and updates the Colour menu in the parent + * AlignFrame (if there is one). Note this action does not including applying + * the colour scheme. + * + * @param filePath + * @return + */ + protected UserColourScheme addNewColourScheme(String filePath) + { + /* + * update the delimited list of user defined colour files in + * Jalview property USER_DEFINED_COLOURS + */ + String defaultColours = Cache.getDefault(USER_DEFINED_COLOURS, + filePath); + if (defaultColours.indexOf(filePath) == -1) + { + if (defaultColours.length() > 0) + { + defaultColours = defaultColours.concat("|"); + } + defaultColours = defaultColours.concat(filePath); + } + Cache.setProperty(USER_DEFINED_COLOURS, defaultColours); + + /* + * construct and register the colour scheme + */ + UserColourScheme ucs = getSchemeFromButtons(); + ColourSchemes.getInstance().registerColourScheme(ucs); + + /* + * update the Colour menu items + */ + if (ap != null) + { + ap.alignFrame.buildColourMenu(); + } + + return ucs; + } + + /** + * Saves the colour scheme to file in XML format + * + * @param path + */ + protected void saveToFile(File toFile) + { + /* + * build a Java model of colour scheme as XML, and + * marshal to file + */ + JalviewUserColours ucs = new JalviewUserColours(); + String name = schemeName.getText(); + ucs.setSchemeName(name); + try + { + PrintWriter out = new PrintWriter(new OutputStreamWriter( + new FileOutputStream(toFile), "UTF-8")); + + for (int i = 0; i < buttonPanel.getComponentCount(); i++) + { + JButton button = (JButton) buttonPanel.getComponent(i); + Colour col = new Colour(); + col.setName(button.getText()); + col.setRGB(Format.getHexString(button.getBackground())); + ucs.getColour().add(col); + } + JAXBContext jaxbContext = JAXBContext + .newInstance(JalviewUserColours.class); + Marshaller jaxbMarshaller = jaxbContext.createMarshaller(); + jaxbMarshaller.marshal( + new ObjectFactory().createJalviewUserColours(ucs), out); + // ucs.marshal(out); + out.close(); + } catch (Exception ex) + { + ex.printStackTrace(); + } + } + + /** + * On cancel, restores the colour scheme that was selected before the dialogue + * was opened + */ + @Override + protected void cancelButton_actionPerformed() + { + ap.alignFrame.changeColour(oldColourScheme); + ap.paintAlignment(true, true); + + try + { + frame.setClosed(true); + } catch (Exception ex) + { + } + } + + /** + * Action on selecting or deselecting the Case Sensitive option. When + * selected, separate buttons are shown for lower case residues, and the panel + * is resized to accommodate them. Also, the checkbox for 'apply colour to all + * lower case' is enabled. + */ + @Override + public void caseSensitive_actionPerformed() + { + boolean selected = caseSensitive.isSelected(); + resetButtonPanel(selected); + lcaseColour.setEnabled(selected); + } +}